| 1. |
- Mattila, Tiina M., et al.
(författare)
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Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe
- 2023
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River. Genome-wide sequencing of 56 ancient hunter-gatherer and early farmer individuals from Stone Age Central and Eastern Europe reveals striking population continuity in the east in contrast to central Europe that displays extensive admixture.
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| 2. |
- Cervantes, Sandra, et al.
(författare)
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Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory
- 2023
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:8
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Tidskriftsartikel (refereegranskat)abstract
- The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.
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| 3. |
- Kastally, Chedly, et al.
(författare)
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Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research
- 2022
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Ingår i: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 109:5, s. 1337-1350
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Tidskriftsartikel (refereegranskat)abstract
- Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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| 4. |
- Mattila, Tiina M, et al.
(författare)
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Extant mammal body masses suggest punctuated equilibrium.
- 2008
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Ingår i: Proc Biol Sci. - : The Royal Society. - 0962-8452. ; 275:1648, s. 2195-9
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Tidskriftsartikel (refereegranskat)abstract
- Is gradual microevolutionary change within species simultaneously the source of macroevolutionary differentiation between species? Since its first publication, Darwin's original idea that phenotypic differences between species develop gradually over time, as the accumulation of small selection-induced changes in successive generations has been challenged by palaeontologists claiming that, instead, new species quickly acquire their phenotypes to remain virtually unchanged until going extinct again. This controversy, widely known as the 'punctuated equilibrium' debate, remained unresolved, largely owing to the difficulty of distinguishing biological species from fossil remains. We analysed body masses of 2143 existing mammal species on a phylogeny comprising 4510 (i.e. nearly all) extant species to estimate rates of gradual (anagenetic) and speciational (cladogenetic) evolution. Our Bayesian estimates from mammals as well as separate sub-clades such as primates and carnivores suggest that gradual evolution is responsible for only a small part of body size variation between mammal species.
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| 5. |
- Mattila, Tiina M., et al.
(författare)
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Impact of demography on linked selection in two outcrossing Brassicaceae species
- 2019
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9:17, s. 9532-9545
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Tidskriftsartikel (refereegranskat)abstract
- Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.
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| 6. |
- Pyhajarvi, Tanja, et al.
(författare)
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New model species for arctic-alpine plant molecular ecology
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:3, s. 637-640
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Arctic and alpine, high latitude and high elevation environments are one of the most stressful environments for species to inhabit. This harshness manifests itself in lower species richness in comparison to more southern vegetation zones (Francis & Currie, 2003). Furthermore, the climatic oscillations-past and predicted-have the most dramatic effect on these ecosystems. For example, in regions of continental ice sheets-the northernmost part of Western Europe and North America-the Arctic species assemblages are no older than a few thousands of years, which is a relatively short period from an evolutionary perspective. Although similar environments may have existed further south during the Ice Age, allowing some preadaptation for the Arctic species, the current habitat is a unique combination of environmental factors such as the climate, soil, bedrock, and photoperiod. Hence, understanding the evolutionary forces shaping Arctic-alpine species will be important for predicting these vulnerable environments' population viability and adaptive potential in the future. In this issue of Molecular Ecology Resources, Nowak et al. (Molecular Ecology Resources)present extensive genome-wide resources for an Arctic-alpine plant Draba nivalis. This adds a valuable new member into the cabbage family models for evolutionary genetics and adaptation studies, to accompany e.g., Arabidopsis (Nature Genetics, 43, 476; Nature, 408, 796), Arabis (Nature Plants, 1, 14023) and Capsella (Nature Genetics, 45, 831). A whole new avenue will open up for molecular ecological studies not only for D. nivalis, but the whole large Draba genus with its diverse ecological and evolutionary characteristics.
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